The easiest, recommended installation is to have a single FarCry app per-site / per-domain, i.e. www.mysite.com.au with the FarCry app running from the webroot (drop the "farcry" folder into the webroot, install, and away you go, no mappings required).
To try to assist with your questions;
1) In the FarCry Core 7.x installer we dropped support for doing a sub-folder install, i.e. www.mysite.com.au/site. It's still possible to manually configure a FarCry app to work this way as the framework support was left in place, but we don't recommend it because the intention is to remove this functionality in FarCry Core 8.x (this will give us both configuration and performance benefits).
If we were in the scenario of having a domain running many types of applications, such as;
... then we would probably run each of these as separate services and use a reverse proxy (e.g. varnish, nginx) to proxy the requests to each different application. It's beneficial to be able to run each search in isolation, so that if you have problems, or if you need to do a deployment, or system updates, you aren't affecting the other separate services. This would be our "ideal" way of solving that problem.
Similarly, if we had a scenario where we had an existing application that was an API, such as;
... then we would most likely want to move the API onto api.mysite.com.au, and create a FarCry app at www.mysite.com.au which is used as the web site for the API.
2) If the FarCry app will be accessible at www.mysite.com.au (not a sub-directory) and your webroot is a folder called "/httpdocs" then yes you upload the unzipped "farcry" folder inside it, giving you "/httpdocs/farcry", no mappings required.
Hope that helps.